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Gallery

Here we show usage examples of the LoVis4u command-line interface. For description of parameters and modes shown on this page visit the Example-driven guide page.

Sample data & Configuration files

The necessary sample data as well as adjustable tool configuration files are provided by lovis4u at the post-install step with the command:
lovis4u --data This copies the lovis4u_data folder to your working directory.

Also important to describe the set of editable configuration files with parameters already adjusted for different tasks and page layout:

  • A4p1 - adjusted for one-column portrait A4 page layout. Figure width - 90mm.
  • A4p2 - adjusted for two-column portrait A4 page layout. Figure width - 190mm.
  • A4L - adjusted for landscape A4 page layout. Figure width - 240mm.
  • standard - flexible width length, scale - 0.05 mm per nucleotide with minimal width - 80mm.
A4 page layout examples

Corresponding PDF file a4page

The full-length visualisation of loci

Miltiple sequences

Visualisation with homology lines and category colours. Figure size: two-column of A4 page publication layout (190mm width).

lovis4u -gff lovis4u_data/guide/gff_files -hl --set-category-colour -c A4p2

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Applying additional functional annotation of proteins using pyhmmer hmmscan. Figure size: two-column of A4 page publication layout (190mm width).

lovis4u -gff lovis4u_data/guide/gff_files -hl --set-category-colour --run-hmmscan -c A4p2

f2

Visualisation with homology lines and category colours. Compact one-column A4 page figure without labelling of conserved proteins (90mm width).

lovis4u -gff lovis4u_data/guide/gff_files -hl --set-category-colour \
    --show-first-feature-label-for  -c A4p1

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One sequence

Visualisation of a single sequence with highlighted protein groups of homologues by different colours and additional functional annotation. Two-column A4 page publication layout (190mm width).

lovis4u -gff lovis4u_data/guide/gff_files/NC_001895.1.gff -hl --set-category-colour -c A4p2 \
    --set-group-colour-for conserved  --run-hmmscan --defence-models PADLOC

f2

Visualisation of a single sequence with GC content and GC skews tracks. Two-column A4 page publication layout (190mm width).

 lovis4u -gff lovis4u_data/guide/gff_files/NC_001895.1.gff -hl --set-category-colour -c A4p2 \
    -gc -gc_skew
f212

Visualisation of user-defined regions

Visualisation of user-defined regions, one region per locus. One-column A4 page layout (90mm width).

lovis4u -gff lovis4u_data/guide/gff_files -c A4p1 --locus-annotation-file lovis4u_data/guide/locus_annotation_table_demo_2.tsv \ 
    -cl-off -hl --set-category-colour

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Visualisation of user-defined regions, multiple regions per locus.

lovis4u -gff lovis4u_data/guide/gff_files  -hl -o lovis4u_output_m_loci  \
    --locus-annotation-file lovis4u_data/guide/locus_annotation_table_demo_1.tsv -cl-off -llp left  -slt

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Non-coding features

Visualisation of loci with non-coding features (tRNAs) and displaying their labels.

lovis4u -gff lovis4u_data/guide/BaselSubset -laf lovis4u_data/guide/locus_annotation_table_trnas.tsv \
     -hl --set-category-colour -c A4p1 --show-first-noncoding-label

fn

Visualisation of genomic signal tracks from sequencing experiments

Starting with version 0.1.0, LoVis4u supports visualisation of genomic signal tracks from sequencing experiments using bedGraph file as input for a single track. We will demonstrate this functionality using three DNA sequencing coverage profiles for BASEL collection phage Bas01.

Visualisation of a single genome with GC content, GC skews tracks and three bedgraph track profiles. Two-column A4 page publication layout (190mm width).

 lovis4u -gff lovis4u_data/guide/BaselCollection/Bas01.gff -c A4p2 -scc -gc -gc_skew \ 
    -bg lovis4u_data/guide/bedgraphs/Bas01_DNA-Seq_WT.bedGraph lovis4u_data/guide/bedgraphs/Bas01_DNA-Seq_1.bedGraph lovis4u_data/guide/bedgraphs/Bas01_DNA-Seq_2.bedGraph \
    -bgl "Bas01 WT | DNA-Seq" "Bas01 E1 | DNA-Seq" "Bas01 E2 | DNA-Seq"

f_bg2

Visualisation of a single genome with GC content, GC skews tracks and three bedgraph track profiles. Multiple windows per image. Two-column A4 page publication layout (190mm width).

lovis4u -gff lovis4u_data/guide/BaselCollection/Bas01.gff -c A4p2 -scc -gc -gc_skew \
 -bg lovis4u_data/guide/bedgraphs/Bas01_DNA-Seq_WT.bedGraph lovis4u_data/guide/bedgraphs/Bas01_DNA-Seq_1.bedGraph lovis4u_data/guide/bedgraphs/Bas01_DNA-Seq_2.bedGraph \ 
-bgl "Bas01 WT | DNA-Seq" "Bas01 E1 | DNA-Seq" "Bas01 E2 | DNA-Seq" \ 
 -w Bas01:1:15000:1,Bas01:16000:31000:1
f_bg2

Visualisation of the Basel collection of phages

For demonstration of LoVis4u's capabilities (and because it is fun), I applied it to the entire Basel collection of 78 Escherichia coli phages (see Maffei et.al. PLOS Biology). In addition, we activate pyhmmer functional annotation of proteins.

lovis4u -gff lovis4u_data/guide/BaselCollection  -hl --set-category-colour -c A4p2 -fw 500  --run-hmmscan

LoVis4u PDF file of the visualisation

Raster image

a4page1

This run also highlights one of LoVis4u key features—its ability to detect clusters of similar proteomes within the input data. Beyond visualisation, LoVis4u generates a matrix of pairwise proteome similarity (see the pipeline description page). The visualisation of this matrix for the Basel collection appears as follows:

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